101
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Hu Y, Shi H, Zhou M, Ren Q, Zhu W, Zhang W, Zhang Z, Zhou C, Liu Y, Ding X, Shen HC, Yan SF, Dey F, Wu W, Zhai G, Zhou Z, Xu Z, Ji Y, Lv H, Jiang T, Wang W, Xu Y, Vercruysse M, Yao X, Mao Y, Yu X, Bradley K, Tan X. Discovery of Pyrido[2,3- b]indole Derivatives with Gram-Negative Activity Targeting Both DNA Gyrase and Topoisomerase IV. J Med Chem 2020; 63:9623-9649. [PMID: 32787097 DOI: 10.1021/acs.jmedchem.0c00768] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rise of multidrug resistant (MDR) Gram-negative (GN) pathogens and the decline of available antibiotics that can effectively treat these severe infections are a major threat to modern medicine. Developing novel antibiotics against MDR GN pathogens is particularly difficult as compounds have to permeate the GN double membrane, which has very different physicochemical properties, and have to circumvent a plethora of resistance mechanisms such as multiple efflux pumps and target modifications. The bacterial type II topoisomerases DNA gyrase (GyrA2B2) and Topoisomerase IV (ParC2E2) are highly conserved targets across all bacterial species and validated in the clinic by the fluoroquinolones. Dual inhibitors targeting the ATPase domains (GyrB/ParE) of type II topoisomerases can overcome target-based fluoroquinolone resistance. However, few ATPase inhibitors are active against GN pathogens. In this study, we demonstrated a successful strategy to convert a 2-carboxamide substituted azaindole chemical scaffold with only Gram-positive (GP) activity into a novel series with also potent activity against a range of MDR GN pathogens. By systematically fine-tuning the many physicochemical properties, we identified lead compounds such as 17r with a balanced profile showing potent GN activity, high aqueous solubility, and desirable PK features. Moreover, we showed the bactericidal efficacy of 17r using a neutropenic mouse thigh infection model.
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Affiliation(s)
| | | | | | - Qingcheng Ren
- WuXi AppTec (Wuhan) Co., Ltd., No. 666 Gaoxin Road, Wuhan East Lake High-tech Development Zone, Hubei 430075, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wen Wang
- MicuRx Pharmaceuticals, Inc. (Shanghai), Floor 3, Building B, 1976 Middle Gaoke Road, Shanghai 201210, China
| | - Yunhua Xu
- MicuRx Pharmaceuticals, Inc. (Shanghai), Floor 3, Building B, 1976 Middle Gaoke Road, Shanghai 201210, China
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102
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Pharmacological and Cosmeceutical Potential of Seaweed Beach-Casts of Macaronesia. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10175831] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Seaweed beach-casts are a seasonal phenomenon that regularly deposits tons of algae biomass on beaches, which are usually disposed of in landfills. The present work aimed to contribute to the valorization of this biomass by studying bioactivities that reveal its potential in the pharmaceutical and/or cosmeceutical industries. Methanol and ethanol extracts and fractions from 15 beach-casts biomass were tested for a range of bioactivities. Eight of the most active samples exhibit IC50 values between 11.38 µg/mL and 19.28 µg/mL and selectivity indexes higher than 3.8, against NCI-H1299 (lung cancer) and T47D (breast cancer). Concerning antiaging potential, all the extracts tested presented UV protection, with SPF values above 30, like the standard sunscreen. Regarding aging-related enzymes, 24 samples were tyrosinase inhibitors exhibiting IC50 values from 9.01 µg/mL to 200.09 µg/mL. Eight extracts inhibited collagenase (IC50 < 248.76 µg/mL), two of them more actively than positive control EDTA (IC50 = 59.26 µg/mL). In addition to UV protection, the cumulative effect of antityrosinase and anticollagenase activities shown by the samples suggest that they may play a significant role in preventing skin photoaging. The results obtained demonstrate the high potential of beach-cast seaweed biomass as sources of cosmetic bioproducts with antiaging effects, and of selective cytotoxic metabolites.
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103
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Park YS, Kim TY, Park H, Lee JH, Nguyen DQ, Hong MK, Lee SH, Kang LW. Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants. Int J Mol Sci 2020; 21:ijms21144926. [PMID: 32664695 PMCID: PMC7404133 DOI: 10.3390/ijms21144926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 01/16/2023] Open
Abstract
The increasing incidence of community- and hospital-acquired infections with multidrug-resistant (MDR) bacteria poses a critical threat to public health and the healthcare system. Although β-lactam antibiotics are effective against most bacterial infections, some bacteria are resistant to β-lactam antibiotics by producing β-lactamases. Among β-lactamases, metallo-β-lactamases (MBLs) are especially worrisome as only a few inhibitors have been developed against them. In MBLs, the metal ions play an important role as they coordinate a catalytic water molecule that hydrolyzes β-lactam rings. We determined the crystal structures of different variants of PNGM-1, an ancient MBL with additional tRNase Z activity. The variants were generated by site-directed mutagenesis targeting metal-coordinating residues. In PNGM-1, both zinc ions are coordinated by six coordination partners in an octahedral geometry, and the zinc-centered octahedrons share a common face. Structures of the PNGM-1 variants confirm that the substitution of a metal-coordinating residue causes the loss of metal binding and β-lactamase activity. Compared with PNGM-1, subclass B3 MBLs lack one metal-coordinating residue, leading to a shift in the metal-coordination geometry from an octahedral to tetrahedral geometry. Our results imply that a subtle change in the metal-binding site of MBLs can markedly change their metal-coordination geometry and catalytic activity.
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Affiliation(s)
- Yoon Sik Park
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Tae Yeong Kim
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Korea; (T.Y.K.); (J.H.L.)
| | - Hyunjae Park
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Korea; (T.Y.K.); (J.H.L.)
| | - Diem Quynh Nguyen
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Myoung-Ki Hong
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Korea; (T.Y.K.); (J.H.L.)
- Correspondence: (S.H.L.); (L.-W.K.); Tel.: +82-31-330-6195 (S.H.L.); +82-2-450-4090 (L.-W.K.)
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
- Correspondence: (S.H.L.); (L.-W.K.); Tel.: +82-31-330-6195 (S.H.L.); +82-2-450-4090 (L.-W.K.)
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104
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Bafna JA, Sans-Serramitjana E, Acosta-Gutiérrez S, Bodrenko IV, Hörömpöli D, Berscheid A, Brötz-Oesterhelt H, Winterhalter M, Ceccarelli M. Kanamycin Uptake into Escherichia coli Is Facilitated by OmpF and OmpC Porin Channels Located in the Outer Membrane. ACS Infect Dis 2020; 6:1855-1865. [PMID: 32369342 DOI: 10.1021/acsinfecdis.0c00102] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Despite decades of therapeutic application of aminoglycosides, it is still a matter of debate if porins contribute to the translocation of the antibiotics across the bacterial outer membrane. Here, we quantified the uptake of kanamycin across the major porin channels OmpF and OmpC present in the outer membrane of Escherichia coli. Our analysis revealed that, despite its relatively large size, about 10-20 kanamycin molecules per second permeate through OmpF and OmpC under a 10 μM concentration gradient, whereas OmpN does not allow the passage. Molecular simulations elucidate the uptake mechanism of kanamycin through these porins. Whole-cell studies with a defined set of E. coli porin mutants provide evidence that translocation of kanamycin via porins is relevant for antibiotic potency. The values are discussed with respect to other antibiotics.
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Affiliation(s)
- Jayesh Arun Bafna
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719Bremen, Germany
| | | | | | - Igor V. Bodrenko
- IOM/CNR, Sezione di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy
| | - Daniel Hörömpöli
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
- German Center for Infection Research (DZIF) Partner Site, D-72076 Tübingen, Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
- German Center for Infection Research (DZIF) Partner Site, D-72076 Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
- German Center for Infection Research (DZIF) Partner Site, D-72076 Tübingen, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719Bremen, Germany
| | - Matteo Ceccarelli
- IOM/CNR, Sezione di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy
- Department of Physics, University of Cagliari, and CNR/IOM, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy
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105
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Skepper CK, Armstrong D, Balibar CJ, Bauer D, Bellamacina C, Benton BM, Bussiere D, De Pascale G, De Vicente J, Dean CR, Dhumale B, Fisher LM, Fuller J, Fulsunder M, Holder LM, Hu C, Kantariya B, Lapointe G, Leeds JA, Li X, Lu P, Lvov A, Ma S, Madhavan S, Malekar S, McKenney D, Mergo W, Metzger L, Moser HE, Mutnick D, Noeske J, Osborne C, Patel A, Patel D, Patel T, Prajapati K, Prosen KR, Reck F, Richie DL, Rico A, Sanderson MR, Satasia S, Sawyer WS, Selvarajah J, Shah N, Shanghavi K, Shu W, Thompson KV, Traebert M, Vala A, Vala L, Veselkov DA, Vo J, Wang M, Widya M, Williams SL, Xu Y, Yue Q, Zang R, Zhou B, Rivkin A. Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria. J Med Chem 2020; 63:7773-7816. [PMID: 32634310 DOI: 10.1021/acs.jmedchem.0c00347] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since their discovery over 5 decades ago, quinolone antibiotics have found enormous success as broad spectrum agents that exert their activity through dual inhibition of bacterial DNA gyrase and topoisomerase IV. Increasing rates of resistance, driven largely by target-based mutations in the GyrA/ParC quinolone resistance determining region, have eroded the utility and threaten the future use of this vital class of antibiotics. Herein we describe the discovery and optimization of a series of 4-(aminomethyl)quinolin-2(1H)-ones, exemplified by 34, that inhibit bacterial DNA gyrase and topoisomerase IV and display potent activity against ciprofloxacin-resistant Gram-negative pathogens. X-ray crystallography reveals that 34 occupies the classical quinolone binding site in the topoisomerase IV-DNA cleavage complex but does not form significant contacts with residues in the quinolone resistance determining region.
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Affiliation(s)
- Colin K Skepper
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Duncan Armstrong
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Carl J Balibar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daniel Bauer
- Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Cornelia Bellamacina
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bret M Benton
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Dirksen Bussiere
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Javier De Vicente
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Charles R Dean
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavesh Dhumale
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - L Mark Fisher
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, U.K
| | - John Fuller
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mangesh Fulsunder
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Lauren M Holder
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Cheng Hu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavin Kantariya
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Guillaume Lapointe
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jennifer A Leeds
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaolin Li
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Peichao Lu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Anatoli Lvov
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Sylvia Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Shravanthi Madhavan
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Swapnil Malekar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - David McKenney
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Louis Metzger
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daniel Mutnick
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jonas Noeske
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Colin Osborne
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Ashish Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Darshit Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Tushar Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Krunal Prajapati
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Katherine R Prosen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daryl L Richie
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alice Rico
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mark R Sanderson
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Shailesh Satasia
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - William S Sawyer
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jogitha Selvarajah
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, U.K
| | - Nirav Shah
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Kartik Shanghavi
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Wei Shu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Katherine V Thompson
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Martin Traebert
- Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Anand Vala
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Lakhan Vala
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Dennis A Veselkov
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Jason Vo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Michael Wang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Marcella Widya
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sarah L Williams
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Yongjin Xu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Qin Yue
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Richard Zang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bo Zhou
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alexey Rivkin
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
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106
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Picconi P, Hind CK, Nahar KS, Jamshidi S, Di Maggio L, Saeed N, Evans B, Solomons J, Wand ME, Sutton JM, Rahman KM. New Broad-Spectrum Antibiotics Containing a Pyrrolobenzodiazepine Ring with Activity against Multidrug-Resistant Gram-Negative Bacteria. J Med Chem 2020; 63:6941-6958. [PMID: 32515951 DOI: 10.1021/acs.jmedchem.0c00328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It is urgent to find new antibiotic classes with activity against multidrug-resistant (MDR) Gram-negative pathogens as the pipeline of antibiotics is essentially empty. Modified pyrrolobenzodiazepines with a C8-linked aliphatic heterocycle provide a new class of broad-spectrum antibacterial agents with activity against MDR Gram-negative bacteria, including WHO priority pathogens. The structure-activity relationship established that the third ring was particularly important for Gram-negative activity. Minimum inhibitory concentrations for the lead compounds ranged from 0.125 to 2 mg/L for MDR Gram-negative, excluding Pseudomonas aeruginosa, and between 0.03 and 1 mg/L for MDR Gram-positive species. The lead compounds were rapidly bactericidal with >5 log reduction in viable count within 4 h for Acinetobacter baumannii and Klebsiella pneumoniae. The lead compound inhibited DNA gyrase in gel-based assays, with an IC50 of 3.16 ± 1.36 mg/L. This study provides a new chemical scaffold for developing novel broad-spectrum antibiotics which can help replenish the pipeline of antibiotics.
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Affiliation(s)
- Pietro Picconi
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Charlotte K Hind
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
| | - Kazi S Nahar
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Shirin Jamshidi
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Lucia Di Maggio
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Naima Saeed
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Bonnie Evans
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
| | - Jessica Solomons
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
| | - Matthew E Wand
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
| | - J Mark Sutton
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
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107
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Mansbach RA, Leus IV, Mehla J, Lopez CA, Walker JK, Rybenkov VV, Hengartner NW, Zgurskaya HI, Gnanakaran S. Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria. J Chem Inf Model 2020; 60:2838-2847. [PMID: 32453589 DOI: 10.1021/acs.jcim.0c00352] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Drug discovery faces a crisis. The industry has used up the "obvious" space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy to combat this is rational approaches to expand the search space without relying on chemical intuition, to avoid rediscovery of similar spaces. In this work, we present proof of concept of an approach to rationally identify a "chemical vocabulary" related to a specific drug activity of interest without employing known rules. We focus on the pressing concern of multidrug resistance in Pseudomonas aeruginosa by searching for submolecules that promote compound entry into this bacterium. By synergizing theory, computation, and experiment, we validate our approach, explain the molecular mechanism behind identified fragments promoting compound entry, and select candidate compounds from an external library that display good permeation ability.
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Affiliation(s)
- Rachael A Mansbach
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Cesar A Lopez
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - John K Walker
- Pharmacology and Physiological Science, School of Medicine, Saint Louis University, Schwitalla Hall, Room M362, St. Louis, Missouri 63104, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Nicolas W Hengartner
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - S Gnanakaran
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
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108
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Motika SE, Ulrich RJ, Geddes EJ, Lee HY, Lau GW, Hergenrother PJ. Gram-Negative Antibiotic Active Through Inhibition of an Essential Riboswitch. J Am Chem Soc 2020; 142:10856-10862. [PMID: 32432858 DOI: 10.1021/jacs.0c04427] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multidrug-resistant Gram-negative (GN) infections for which there are few available treatment options are increasingly common. The development of new antibiotics for these pathogens is challenging because of the inability of most small molecules to accumulate inside GN bacteria. Using recently developed predictive guidelines for compound accumulation in Escherichia coli, we have converted the antibiotic Ribocil C, which targets the flavin mononucleotide (FMN) riboswitch, from a compound lacking whole-cell activity against wild-type GN pathogens into a compound that accumulates to a high level in E. coli, is effective against Gram-negative clinical isolates, and has efficacy in mouse models of GN infections. This compound allows for the first assessment of the translational potential of FMN riboswitch binders against wild-type Gram-negative bacteria.
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Affiliation(s)
| | | | | | | | - Gee W Lau
- Department of Pathobiology, University of Illinois, Urbana, Illinois 61802, United States
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109
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Hoffman PS. Antibacterial Discovery: 21st Century Challenges. Antibiotics (Basel) 2020; 9:antibiotics9050213. [PMID: 32353943 PMCID: PMC7277910 DOI: 10.3390/antibiotics9050213] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
It has been nearly 50 years since the golden age of antibiotic discovery (1945–1975) ended; yet, we still struggle to identify novel drug targets and to deliver new chemical classes of antibiotics to replace those rendered obsolete by drug resistance. Despite herculean efforts utilizing a wide range of antibiotic discovery platform strategies, including genomics, bioinformatics, systems biology and postgenomic approaches, success has been at best incremental. Obviously, finding new classes of antibiotics is really hard, so repeating the old strategies, while expecting different outcomes, seems to boarder on insanity. The key questions dealt with in this review include: (1) If mutation based drug resistance is the major challenge to any new antibiotic, is it possible to find drug targets and new chemical entities that can escape this outcome; (2) Is the number of novel chemical classes of antibacterials limited by the number of broad spectrum drug targets; and (3) If true, then should we focus efforts on subgroups of pathogens like Gram negative or positive bacteria only, anaerobic bacteria or other group where the range of common essential genes is likely greater?. This review also provides some examples of existing drug targets that appear to escape the specter of mutation based drug resistance, and provides examples of some intermediate spectrum strategies as well as modern molecular and genomic approaches likely to improve the odds of delivering 21st century medicines to combat multidrug resistant pathogens.
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Affiliation(s)
- Paul S Hoffman
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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110
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Liu K, Huigens RW. Instructive Advances in Chemical Microbiology Inspired by Nature's Diverse Inventory of Molecules. ACS Infect Dis 2020; 6:541-562. [PMID: 31842540 PMCID: PMC7346871 DOI: 10.1021/acsinfecdis.9b00413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Natural product antibiotics have played an essential role in the treatment of bacterial infection in addition to serving as useful tools to explore the intricate biology of bacteria. Our current arsenal of antibiotics operate through the inhibition of well-defined bacterial targets critical for replication and growth. Pathogenic bacteria effectively utilize a diversity of mechanisms that lead to acquired resistance and/or innate tolerance toward antibiotic therapies, which can result in devastating consequences to human life. Several research groups have established innovative programs that work at the chemistry-biology interface to develop new molecules that aim to define and address concerns related to antibiotic resistance and tolerance. In this Review, we present recent progress by select research groups that highlight a diversity of integrated chemical biology and medicinal chemistry approaches aimed at the development and utilization of chemical tools that have led to promising new microbiological insights that may lead to significant clinical advances regarding the treatment of pathogenic bacteria.
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Affiliation(s)
- Ke Liu
- 1345 Center Drive, Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Robert W. Huigens
- 1345 Center Drive, Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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111
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Wu C, Xia L, Huang W, Xu Y, Gu Y, Liu C, Ji L, Li W, Wu Y, Zhou K, Feng X. Pentamidine sensitizes FDA-approved non-antibiotics for the inhibition of multidrug-resistant Gram-negative pathogens. Eur J Clin Microbiol Infect Dis 2020; 39:1771-1779. [PMID: 32242313 DOI: 10.1007/s10096-020-03881-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022]
Abstract
Pentamidine sensitizes FDA-approved antibiotics to combat Gram-negative pathogens. We screened 1374 FDA-approved non-antibiotics for their ability to be sensitized by pentamidine against Escherichia coli. We identified mitomycin C and mefloquine as potent hits effective against multiple drug-resistant, Gram-negative bacteria. Killing kinetics and an in vivo model with Caenorhabditis elegans (C. elegans) revealed that such combinations produced synergy against colistin-resistant Enterobacter cloacae (E. cloacae). These findings suggest combinations of FDA-approved non-antibiotics, and pentamidine can be repurposed into new antimicrobial agents.
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Affiliation(s)
- Chenxuan Wu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China
| | - Ling Xia
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China
| | - Wei Huang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China
| | - Yangfan Xu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China
| | - Yuanxin Gu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China
| | - Chang Liu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China
| | - Luting Ji
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China
| | - Wenyao Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China
| | - Yandong Wu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China.,The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Xinxin Feng
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha, 410082, China.
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112
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Cheng AV, Schrank CL, Escobar IE, Mylonakis E, Wuest WM. Addition of ethylamines to the phenols of bithionol and synthetic retinoids does not elicit activity in gram-negative bacteria. Bioorg Med Chem Lett 2020; 30:127099. [PMID: 32171615 DOI: 10.1016/j.bmcl.2020.127099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/04/2020] [Accepted: 03/07/2020] [Indexed: 12/30/2022]
Abstract
Our labs have demonstrated the activity of bithionol and synthetic retinoids against methicillin-resistant Staphylococcus aureus (MRSA), as well as their membrane-acting mechanism of action. However, the compounds lack activity in gram-negative species. Herein, we apply a known strategy for converting gram-positive agents into broad-spectrum therapies: addition of an alkylamine. By appending an alkylamine to the phenols of these known membrane disruptors, we test whether this approach is applicable to our compounds. Ultimately, biological testing in four MRSA strains and three gram-negative species showed abolished or diminished activity in all our analogs compared to their parent compounds and no gram-negative activity. Thus, we find that alkylamines would not elicit broad-spectrum activity from bithionol or CD437 derivatives.
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Affiliation(s)
- Ana V Cheng
- Department of Chemistry, Emory University, United States.
| | | | - Iliana E Escobar
- Division of Infectious Diseases, Rhode Island Hospital, United States.
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113
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Fisher JF, Mobashery S. Constructing and deconstructing the bacterial cell wall. Protein Sci 2020; 29:629-646. [PMID: 31747090 PMCID: PMC7021008 DOI: 10.1002/pro.3737] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the β-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β-lactams. This review summarizes how the β-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
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114
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Laurent Q, Berthet M, Cheng Y, Sakai N, Barluenga S, Winssinger N, Matile S. Probing for Thiol-Mediated Uptake into Bacteria. Chembiochem 2020; 21:69-73. [PMID: 31603284 DOI: 10.1002/cbic.201900378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Indexed: 01/02/2023]
Abstract
Cellular uptake mediated by cyclic oligochalcogenides (COCs) is emerging as a conceptually innovative method to penetrate mammalian cells. Their mode of action is based on dynamic covalent oligochalcogenide exchange with cellular thiols. To test thiol-mediated uptake in bacteria, five antibiotics have been equipped with up to three different COCs: One diselenolane and two dithiolanes. We found that the COCs do not activate antibiotics in Gram-negative bacteria. In Gram-positive bacteria, the COCs inactivate antibiotics that act in the cytoplasm and reduce the activity of antibiotics that act on the cell surface. These results indicate that thiol-mediated uptake operates in neither of the membranes of bacteria. COCs are likely to exchange with thiols on the inner, maybe also on the outer membrane, but do not move on. Concerning mammalian cells, the absence of a COC-mediated uptake into bacteria observed in this study disfavors trivial mechanisms, such as passive diffusion, and supports the existence of more sophisticated, so far poorly understood uptake pathways.
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Affiliation(s)
- Quentin Laurent
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Mathéo Berthet
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Yangyang Cheng
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Naomi Sakai
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Sofia Barluenga
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Stefan Matile
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
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115
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Georgiadis MO, Kourbeli V, Papanastasiou IP, Tsotinis A, Taylor MC, Kelly JM. Synthesis and evaluation of novel 2,4-disubstituted arylthiazoles against T. brucei. RSC Med Chem 2019; 11:72-84. [PMID: 33479605 PMCID: PMC7522794 DOI: 10.1039/c9md00478e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/22/2019] [Indexed: 01/10/2023] Open
Abstract
2-{2-[3-(1-Adamantyl)-4-fluorophenyl]thiazol-4-yl}ethan-1-amine (1a) and 2-{2-[4-(1-adamantyl)phenyl]thiazol-4-yl}ethan-1-amine (2a) exhibit activity against T. brucei in the range of IC50 = 0.42 μM and IC50 = 0.80 μM, respectively.
The design, synthesis and pharmacological evaluation of the 4-substituted-2-[3-(adamant-1-yl)-4-fluorophenyl]thiazoles 1a–j, the 4-substituted-2-[4-(adamant-1-yl)phenyl]thiazoles 2a–h, the 2-substituted-4-[4-(adamant-1-yl)phenyl]thiazoles 3a–e, the N-substituted 2-phenylthiazol-4-ethylamides 4a, b and the N-substituted 4-phenylthiazol-2-ethylamides 4c, d is described. Compounds 1a and 2a exhibit trypanocidal activity in the range of IC50 = 0.42 μM and IC50 = 0.80 μM, respectively. Both of these derivatives bear a lipophilic end, which consists of a 4-(1-adamantyl) phenyl or a 3-(1-adamantyl)phenyl moiety, a 1,3-thiazole ring and a functional end, which comprises of an alkylamine and can be considered as promising candidates for the treatment of Trypanosoma brucei infections.
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Affiliation(s)
- Markos-Orestis Georgiadis
- Division of Pharmaceutical Chemistry , Department of Pharmacy , School of Health Sciences , National and Kapodistrian University of Athens , Panepistimioupoli-Zografou , 157 84 Athens , Greece .
| | - Violeta Kourbeli
- Division of Pharmaceutical Chemistry , Department of Pharmacy , School of Health Sciences , National and Kapodistrian University of Athens , Panepistimioupoli-Zografou , 157 84 Athens , Greece .
| | - Ioannis P Papanastasiou
- Division of Pharmaceutical Chemistry , Department of Pharmacy , School of Health Sciences , National and Kapodistrian University of Athens , Panepistimioupoli-Zografou , 157 84 Athens , Greece .
| | - Andrew Tsotinis
- Division of Pharmaceutical Chemistry , Department of Pharmacy , School of Health Sciences , National and Kapodistrian University of Athens , Panepistimioupoli-Zografou , 157 84 Athens , Greece .
| | - Martin C Taylor
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street , London WC1 E7HT , UK
| | - John M Kelly
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street , London WC1 E7HT , UK
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116
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Ferreira RJ, Kasson PM. Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics. ACS Infect Dis 2019; 5:2096-2104. [PMID: 31593635 DOI: 10.1021/acsinfecdis.9b00201] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Crossing the Gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer membrane uptake of drug-like molecules, which we combine with a new medium-throughput experimental assay of outer membrane vesicle swelling. Parallel molecular dynamics simulations of compound uptake through Escherichia coli (E. coli) OmpF are used to successfully and quantitatively predict experimental permeabilities measured via either outer membrane swelling or prior liposome-swelling measurements. These simulations are analyzed using an inhomogeneous solubility-diffusion model to yield predictions of permeability. For most polar molecules we test, outer membrane permeability also correlates well with whole-cell uptake. The ability to accurately predict and measure outer membrane uptake of a wide variety of small molecules will enable simpler determination of which molecular scaffolds and which derivatives are most promising prior to extensive chemical synthesis. It will also assist in formulating a more systematic understanding of the chemical determinants of outer membrane permeability.
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Affiliation(s)
- Ricardo J. Ferreira
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Peter M. Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
- Departments of Biomedical Engineering and Molecular Physiology and Biological Physics, University of Virginia, Box 800886, Charlottesville, Virginia 22908, United States
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117
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Parker EN, Drown BS, Geddes EJ, Lee HY, Ismail N, Lau GW, Hergenrother PJ. Implementation of permeation rules leads to a FabI inhibitor with activity against Gram-negative pathogens. Nat Microbiol 2019; 5:67-75. [PMID: 31740764 PMCID: PMC6953607 DOI: 10.1038/s41564-019-0604-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 10/04/2019] [Indexed: 01/17/2023]
Abstract
Gram-negative bacterial infections are a significant public health concern, and the lack of new drug classes for these pathogens is linked to the inability of most drug leads to accumulate inside Gram-negative bacteria1-7. Here, we report the development of a web application-eNTRyway-that predicts compound accumulation (in Escherichia coli) from its structure. In conjunction with structure-activity relationships and X-ray data, eNTRyway was utilized to re-design Debio-1452-a Gram-positive-only antibiotic8-into versions that accumulate in E. coli and possess antibacterial activity against high-priority Gram-negative pathogens. The lead compound Debio-1452-NH3 operates as an antibiotic via the same mechanism as Debio-1452, namely potent inhibition of the enoyl-acyl carrier protein reductase FabI, as validated by in vitro enzyme assays and the generation of bacterial isolates with spontaneous target mutations. Debio-1452-NH3 is well tolerated in vivo, reduces bacterial burden in mice and rescues mice from lethal infections with clinical isolates of Acinetobacter baumannii, Klebsiella pneumoniae and E. coli. This work provides tools for the facile discovery and development of high-accumulating compounds in E. coli, and a general blueprint for the conversion of Gram-positive-only compounds into broad-spectrum antibiotics.
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Affiliation(s)
- Erica N Parker
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bryon S Drown
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emily J Geddes
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hyang Yeon Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nahed Ismail
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Gee W Lau
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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118
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Abrusán G, Marsh JA. Ligands and Receptors with Broad Binding Capabilities Have Common Structural Characteristics: An Antibiotic Design Perspective. J Med Chem 2019; 62:9357-9374. [PMID: 31188598 PMCID: PMC6858282 DOI: 10.1021/acs.jmedchem.9b00220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Indexed: 01/08/2023]
Abstract
The spread of antibiotic resistance is one of the most serious global public-health problems. Here we show that a particular class of homomers with binding sites spanning multiple protein chains is particularly suitable for targeting by broad-spectrum antibacterial agents because due to the slow evolutionary change of such binding pockets, ligands of such homomers are much more likely to bind their homologs than ligands of monomers, or homomers with a single-chain binding site. Additionally, using de novo ligand design and deep learning, we show that the chemical compounds that can bind several different receptors have common structural characteristics and that halogens and fragments similar to the building blocks existing antimicrobials are overrepresented in them. Finally, we show that binding multiple receptors selects for flexible compounds, which are less likely to accumulate in Gram-negative bacteria; thus there is trade-off between reducing the emergence of resistance by multitargeting and broad-spectrum antibacterial activity.
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Affiliation(s)
- György Abrusán
- MRC Human Genetics Unit, Institute
of Genetics and Molecular Medicine, University
of Edinburgh, Crewe Road, Edinburgh EH4 2XU, U.K.
| | - Joseph A. Marsh
- MRC Human Genetics Unit, Institute
of Genetics and Molecular Medicine, University
of Edinburgh, Crewe Road, Edinburgh EH4 2XU, U.K.
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119
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Wang X, Chen J, Wang W, Jaunarajs A, Wang X. Tryptoline-based benzothiazoles re-sensitize MRSA to β-lactam antibiotics. Bioorg Med Chem 2019; 27:115095. [PMID: 31521461 PMCID: PMC6779328 DOI: 10.1016/j.bmc.2019.115095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 01/03/2023]
Abstract
Resistance-modifying agents (RMAs) offer a promising solution to combat bacterial antibiotic resistance. Here we report the discovery and structure-activity relationships of a new class of RMAs with a novel tryptoline-based benzothiazole scaffold. Our most potent compound in this series (4ad) re-sensitizes multiple MRSA strains to cephalosporins at low concentrations (2 μg/mL) and has low mammalian cytotoxicity with a half growth inhibitory concentration (GI50) > 100 μg/mL in human cervical carcinoma (HeLa) cells. In addition, the same core scaffold with different substitutions also gives good antibacterial activity against MRSA.
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Affiliation(s)
- Xinfeng Wang
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Jinsen Chen
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Wei Wang
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Anna Jaunarajs
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Xiang Wang
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States.
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120
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Antonoplis A, Zang X, Wegner T, Wender PA, Cegelski L. Vancomycin-Arginine Conjugate Inhibits Growth of Carbapenem-Resistant E. coli and Targets Cell-Wall Synthesis. ACS Chem Biol 2019; 14:2065-2070. [PMID: 31479234 DOI: 10.1021/acschembio.9b00565] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The emergence of multi-drug-resistant Gram-negative bacteria, including carbapenem-resistant Enterobacteriaceae, is a major health problem that necessitates the development of new antibiotics. Vancomycin inhibits cell-wall synthesis in Gram-positive bacteria but is generally ineffective against Gram-negative bacteria and is unable to penetrate the outer membrane barrier. In an effort to determine whether vancomycin and other antibiotics effective against Gram-positive bacteria could, through modification, be rendered effective against Gram-negative bacteria, we discovered that the covalent attachment of a single arginine to vancomycin yielded conjugates with order-of-magnitude improvements in activity against Gram-negative bacteria, including pathogenic E. coli. The vancomycin-arginine conjugate (V-R) exhibited efficacy against actively growing bacteria, induced the loss of rod cellular morphology, and resulted in the intracellular accumulation of peptidoglycan precursors, all consistent with cell-wall synthesis disruption as its mechanism of action. Membrane permeabilization studies demonstrated an enhanced outer membrane permeability of V-R as compared with vancomycin. The conjugate exhibited no mammalian cell toxicity or hemolytic activity in MTT and hemolysis assays. Our study introduces a new vancomycin derivative effective against Gram-negative bacteria and underscores the broader potential of generating new antibiotics through combined mode-of-action and synthesis-informed design studies.
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Affiliation(s)
- Alexandra Antonoplis
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Xiaoyu Zang
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tristan Wegner
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Paul A. Wender
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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121
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Chen C, Yang K. Ebselen bearing polar functionality: Identification of potent antibacterial agents against multidrug-resistant Gram-negative bacteria. Bioorg Chem 2019; 93:103286. [PMID: 31585265 DOI: 10.1016/j.bioorg.2019.103286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/20/2019] [Accepted: 09/15/2019] [Indexed: 01/06/2023]
Abstract
Antibiotic-resistant bacteria has become one of the greatest challenges to global human health today. Innovative strategies are needed to identify new therapeutic leads to tackle infections of drug-resistant Gram-negative bacteria. We herein synthesize a series of EB analogues to investigate their antibacterial activities. Select polar functionality at N-terminus of EB exhibited higher activities against multi-drug-resistant Gram-negative pathogens, including E. coli, P. aeruginosa and K. pneumoniae. EB analogue 4g and 4i exhibited potent antibacterial activities against E. coli-ESBL (MIC = 1-4 µg/mL) and E. coli producing NDM-1 (MIC = 4-32 µg/mL), which is superior to the traditional antibiotics (cefazolin, imipenem). Furthermore, the time-kill kinetics studies and the inhibition zone tests indicated that analogue 4i effectively and rapidly cause death of E. coli-ESBL and E. coli-NDM-1. Additionally, accumulation assays and SEM images showed that 4i could permeate bacterial membranes, leading to an irregular cell morphology. Importantly, bacterial resistance for analogue 4i was difficult to induce against E. coli-ESBL. EB analogues here reported low cytotoxicity against L-929 cells and mice model in vivo. We believe that EB analogues with polar functionality could play a pivotal role in the development of novel antibacterial agents in eradicating multi-drug-resistant Gram-negative pathogens infections.
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Affiliation(s)
- Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi'an 710127, PR China
| | - Kewu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi'an 710127, PR China.
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Seol G, Park H, Ahn Y, Kang L. Crystal Structure of Enoyl‐Acyl Carrier Protein Reductase (FabI) fromAcinetobacter baumanniias a Target for Broad‐Spectrum Antibacterial Drug. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gyunbo Seol
- Department of Biological SciencesKonkuk University Seoul 05029 Republic of Korea
| | - Hyunjae Park
- Department of Biological SciencesKonkuk University Seoul 05029 Republic of Korea
| | - Yeh‐Jin Ahn
- Department of BiotechnologySangmyung University Seoul 03016 Republic of Korea
| | - Lin‐Woo Kang
- Department of Biological SciencesKonkuk University Seoul 05029 Republic of Korea
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123
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Andrews LD, Kane TR, Dozzo P, Haglund CM, Hilderbrandt DJ, Linsell MS, Machajewski T, McEnroe G, Serio AW, Wlasichuk KB, Neau DB, Pakhomova S, Waldrop GL, Sharp M, Pogliano J, Cirz RT, Cohen F. Optimization and Mechanistic Characterization of Pyridopyrimidine Inhibitors of Bacterial Biotin Carboxylase. J Med Chem 2019; 62:7489-7505. [PMID: 31306011 DOI: 10.1021/acs.jmedchem.9b00625] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A major challenge for new antibiotic discovery is predicting the physicochemical properties that enable small molecules to permeate Gram-negative bacterial membranes. We have applied physicochemical lessons from previous work to redesign and improve the antibacterial potency of pyridopyrimidine inhibitors of biotin carboxylase (BC) by up to 64-fold and 16-fold against Escherichia coli and Pseudomonas aeruginosa, respectively. Antibacterial and enzyme potency assessments in the presence of an outer membrane-permeabilizing agent or in efflux-compromised strains indicate that penetration and efflux properties of many redesigned BC inhibitors could be improved to various extents. Spontaneous resistance to the improved pyridopyrimidine inhibitors in P. aeruginosa occurs at very low frequencies between 10-8 and 10-9. However, resistant isolates had alarmingly high minimum inhibitory concentration shifts (16- to >128-fold) compared to the parent strain. Whole-genome sequencing of resistant isolates revealed that either BC target mutations or efflux pump overexpression can lead to the development of high-level resistance.
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Affiliation(s)
- Logan D Andrews
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Timothy R Kane
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Paola Dozzo
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Cat M Haglund
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Darin J Hilderbrandt
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Martin S Linsell
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Timothy Machajewski
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Glen McEnroe
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Alisa W Serio
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Kenneth B Wlasichuk
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - David B Neau
- Northeastern Collaborative Access Team , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Svetlana Pakhomova
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Grover L Waldrop
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Marc Sharp
- Linnaeus Bioscience Inc. , 3210 Merryfield Row , San Diego , California 92121 , United States
| | - Joe Pogliano
- Linnaeus Bioscience Inc. , 3210 Merryfield Row , San Diego , California 92121 , United States.,University of California, San Diego , 9500 Gilman Drive , La Jolla, San Diego , California 92093 , United States
| | - Ryan T Cirz
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Frederick Cohen
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
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124
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Cohen F, Aggen JB, Andrews LD, Assar Z, Boggs J, Choi T, Dozzo P, Easterday AN, Haglund CM, Hildebrandt DJ, Holt MC, Joly K, Jubb A, Kamal Z, Kane TR, Konradi AW, Krause KM, Linsell MS, Machajewski TD, Miroshnikova O, Moser HE, Nieto V, Phan T, Plato C, Serio AW, Seroogy J, Shakhmin A, Stein AJ, Sun AD, Sviridov S, Wang Z, Wlasichuk K, Yang W, Zhou X, Zhu H, Cirz RT. Optimization of LpxC Inhibitors for Antibacterial Activity and Cardiovascular Safety. ChemMedChem 2019; 14:1560-1572. [DOI: 10.1002/cmdc.201900287] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/03/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Frederick Cohen
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - James B. Aggen
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Logan D. Andrews
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Zahra Assar
- Cayman Chemical Co. 1180 East Ellsworth Ann Arbor MI 48108 USA
| | - Jen Boggs
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Taylor Choi
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Paola Dozzo
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | | | - Cat M. Haglund
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | | | - Melissa C. Holt
- Cayman Chemical Co. 1180 East Ellsworth Ann Arbor MI 48108 USA
| | - Kristin Joly
- Plato BioPharma Inc. 7581 West 103rd Avenue, Unit 300 Westminster CO 80021 USA
| | - Adrian Jubb
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Zeeshan Kamal
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Timothy R. Kane
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | | | - Kevin M. Krause
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Martin S. Linsell
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | | | | | - Heinz E. Moser
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Vincent Nieto
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Thu Phan
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Craig Plato
- Plato BioPharma Inc. 7581 West 103rd Avenue, Unit 300 Westminster CO 80021 USA
| | - Alisa W. Serio
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Julie Seroogy
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Anton Shakhmin
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Adam J. Stein
- Cayman Chemical Co. 1180 East Ellsworth Ann Arbor MI 48108 USA
| | - Alex D. Sun
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | | | - Zhan Wang
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Kenneth Wlasichuk
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Wen Yang
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Xiaoming Zhou
- Pharmaron Inc. 6 Tai-He Road, BDA Beijing 100176 China
| | - Hai Zhu
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Ryan T. Cirz
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
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125
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Breaching the Barrier: Quantifying Antibiotic Permeability across Gram-negative Bacterial Membranes. J Mol Biol 2019; 431:3531-3546. [DOI: 10.1016/j.jmb.2019.03.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/29/2019] [Accepted: 03/28/2019] [Indexed: 11/22/2022]
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126
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Hernandez LW, Sarlah D. Empowering Synthesis of Complex Natural Products. Chemistry 2019; 25:13248-13270. [DOI: 10.1002/chem.201901808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/08/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Lucas W. Hernandez
- Department of Chemistry University of Illinois at Urbana-Champaign 600 South Mathews Avenue 270 RAL, Box 107-5 Urbana IL 61801 USA
| | - David Sarlah
- Department of Chemistry University of Illinois at Urbana-Champaign 600 South Mathews Avenue 270 RAL, Box 107-5 Urbana IL 61801 USA
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127
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Ilbeigi G, Kariminik A, Moshafi MH. The Antibacterial Activities of NiO Nanoparticles Against Some Gram-Positive and Gram-Negative Bacterial Strains. INTERNATIONAL JOURNAL OF BASIC SCIENCE IN MEDICINE 2019. [DOI: 10.15171/ijbsm.2019.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Introduction: Given the increasing rate of antibiotic resistance among bacterial strains, many researchers have been working to produce new and efficient and inexpensive antibacterial agents. It has been reported that some nanoparticles may be used as novel antimicrobial agents.Here, we evaluated antibacterial properties of nickel oxide (NiO) nanoparticles. Methods: NiO nanoparticles were synthesized using microwave method. In order to control the quality and morphology of nanoparticles, XRD (X-ray diffraction) and SEM (scanning electronmicroscope) were utilized. The antibacterial properties of the nanoparticles were assessed against eight common bacterial strains using agar well diffusion assay. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were measured. Antibiotic resistance pattern of the bacteria to nine antibiotics was obtained by Kirby-Bauer disk diffusion method. Results: The crystalline size and diameter (Dc) of NiO nanoparticles were obtained 40-60 nm. The nanoparticles were found to inhibit the growth of both gram-positive and gram-negative bacteria with higher activity against gram-positive organisms. Among bacterial strains, maximum sensitivity was observed in Staphylococcus epidermidis with MIC and MBC of 0.39 and 0.78 mg/mL, respectively. The bacteria had high resistance to cefazolin, erythromycin, rifampicin,ampicillin, penicillin and streptomycin.Conclusion: NiO nanoparticles exhibited remarkable antibacterial properties against gram positive and gram-negative bacteria and can be a new treatment for human pathogenic and antibiotic-resistant bacteria.
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Affiliation(s)
- Ghazaleh Ilbeigi
- Department of Microbiology, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Ashraf Kariminik
- Department of Microbiology, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Mohammad Hasan Moshafi
- Pharmacology Department, School of Medicine, Kerman University of Medical Sciences and Health Services, Kerman, Iran
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128
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Defects in Efflux ( oprM), β-Lactamase ( ampC), and Lipopolysaccharide Transport ( lptE) Genes Mediate Antibiotic Hypersusceptibility of Pseudomonas aeruginosa Strain Z61. Antimicrob Agents Chemother 2019; 63:AAC.00784-19. [PMID: 31036686 DOI: 10.1128/aac.00784-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 02/08/2023] Open
Abstract
Antibiotic hypersensitive bacterial mutants (e.g., Escherichia coli imp) are used to investigate intrinsic resistance and are exploited in antibacterial discovery to track weak antibacterial activity of novel inhibitor compounds. Pseudomonas aeruginosa Z61 is one such drug-hypersusceptible strain generated by chemical mutagenesis, although the genetic basis for hypersusceptibility is not fully understood. Genome sequencing of Z61 revealed nonsynonymous single-nucleotide polymorphisms in 153 genes relative to its parent strain, and three candidate mutations (in oprM, ampC, and lptE) predicted to mediate hypersusceptibility were characterized. The contribution of these mutations was confirmed by genomic restoration of the wild-type sequences, individually or in combination, in the Z61 background. Introduction of the lptE mutation or genetic inactivation of oprM and ampC genes alone or together in the parent strain recapitulated drug sensitivities. This showed that disruption of oprM (which encodes a major outer membrane efflux pump channel) increased susceptibility to pump substrate antibiotics, that inactivation of the inducible β-lactamase gene ampC contributed to β-lactam susceptibility, and that mutation of the lipopolysaccharide transporter gene lptE strongly altered the outer membrane permeability barrier, causing susceptibility to large antibiotics such as rifampin and also to β-lactams.
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129
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Díaz-Roa A, Espinoza-Culupú A, Torres-García O, Borges MM, Avino IN, Alves FL, Miranda A, Patarroyo MA, da Silva PI, Bello FJ. Sarconesin II, a New Antimicrobial Peptide Isolated from Sarconesiopsis magellanica Excretions and Secretions. Molecules 2019; 24:E2077. [PMID: 31159162 PMCID: PMC6600161 DOI: 10.3390/molecules24112077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/11/2019] [Accepted: 04/20/2019] [Indexed: 01/13/2023] Open
Abstract
Antibiotic resistance is at dangerous levels and increasing worldwide. The search for new antimicrobial drugs to counteract this problem is a priority for health institutions and organizations, both globally and in individual countries. Sarconesiopsis magellanica blowfly larval excretions and secretions (ES) are an important source for isolating antimicrobial peptides (AMPs). This study aims to identify and characterize a new S. magellanica AMP. RP-HPLC was used to fractionate ES, using C18 columns, and their antimicrobial activity was evaluated. The peptide sequence of the fraction collected at 43.7 min was determined by mass spectrometry (MS). Fluorescence and electronic microscopy were used to evaluate the mechanism of action. Toxicity was tested on HeLa cells and human erythrocytes; physicochemical properties were evaluated. The molecule in the ES was characterized as sarconesin II and it showed activity against Gram-negative (Escherichia coli MG1655, Pseudomonas aeruginosa ATCC 27853, P. aeruginosa PA14) and Gram-positive (Staphylococcus aureus ATCC 29213, Micrococcus luteus A270) bacteria. The lowest minimum inhibitory concentration obtained was 1.9 μM for M. luteus A270; the AMP had no toxicity in any cells tested here and its action in bacterial membrane and DNA was confirmed. Sarconesin II was documented as a conserved domain of the ATP synthase protein belonging to the Fli-1 superfamily. The data reported here indicated that peptides could be alternative therapeutic candidates for use in infections against Gram-negative and Gram-positive bacteria and eventually as a new resource of compounds for combating multidrug-resistant bacteria.
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Affiliation(s)
- Andrea Díaz-Roa
- Special Laboratory for Applied Toxinology (LETA), Butantan Institute, São Paulo CEP 05503-900, SP, Brazil.
- Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-900, SP, Brazil.
- PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá 111221, Colombia.
| | - Abraham Espinoza-Culupú
- Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-900, SP, Brazil.
- Bacteriology Laboratory, Butantan Institute, São Paulo CEP 05503-900, SP, Brazil.
| | | | - Monamaris M Borges
- Bacteriology Laboratory, Butantan Institute, São Paulo CEP 05503-900, SP, Brazil.
| | - Ivan N Avino
- Special Laboratory of Cell Cycle (LECC), Butantan Institute, São Paulo CEP 05503-900, SP, Brazil.
| | - Flávio L Alves
- Biophysics Department, UNIFESP, São Paulo CEP 04023-062, Brazil.
| | - Antonio Miranda
- Biophysics Department, UNIFESP, São Paulo CEP 04023-062, Brazil.
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá 111321, Colombia.
- Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 112111, Colombia.
| | - Pedro I da Silva
- Special Laboratory for Applied Toxinology (LETA), Butantan Institute, São Paulo CEP 05503-900, SP, Brazil.
- Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-900, SP, Brazil.
| | - Felio J Bello
- Faculty of Agricultural and Livestock Sciences, Veterinary Medicine Programme, Universidad de La Salle, Bogotá 110141, Colombia.
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130
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Isayenko OY, Knysh OV, Kotsar OV, Ryzhkova TN, Dyukareva GI. Evaluation of anti-microbial activity of filtrates of Lactobacillus rhamnosus and Saccharomyces boulardii against antibiotic-resistant gram-negative bacteria. REGULATORY MECHANISMS IN BIOSYSTEMS 2019. [DOI: 10.15421/021937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The article presents the results of the first study on the influence of biologically active substances Lactobacillus rhamnosus GG ATCC 53103 and Saccharomyces boulardii, obtained according to the author`s method, on growth of gram-negative bacteria with broad medical resistance: Pseudomonas aeruginosa PR, Klebsiella pneumoniae PR, Lelliottia amnigena (Enterobacter amnigenus) PR using the spectrophotometric method. Disintegrates of L. rhamnosus GG and S. boulardii were obtained using low-frequency ultrasound processing of suspension of probiotic strains, and metabolites – through cultivation of lactobacteria and saccharomycetes in disintegrates of probiotic microorganisms. To samples of test-cultures with studied filtrates of disintegrates or metabolites we added growth medium and cultivated them (period of monitoring was 5- and 24-hours). Results of the studies were expressed as the percentage of inhibition of increment in polyresistant gram-negative bacteria under the impact of biologically active substances of probiotic microorganisms. Five-hour incubation of test-strains with the studied samples of lactobacteria led to inhibition of their growth properties by 85.6–96.7%. Growth of bacteria under the impact of substances of saccharomycetes was inhibted by 45.1–92.5%. Twenty-four hour exposure of the test-cultures in filtrates of L. rhamnosus GG and S. boulardii caused 100% inhibition of P. aeruginosa and L. amnigena polyresistant strains. Temporal interval of cultivation directly proportionally affected the extent of inhibition of growth of microorganisms: we determined direct correlation dependence within 0.789–0.991. Maximum inhibition of increment of the studied pathogens was observed under the influence of metabolites of lactobacteria, obtained by cultivating primary producers in their disintegrate. We determined a high level of anti-microbial activity of metabolites from L. rhamnosus GG and S. boulardii obtained by cultivation of probiotics in disintegrates against bacteria resistant to a broad range of preparations, which allows us to consider these substances as promising for development of anti-microbial preparations of a new generation against etiologically significant antibiotic-resistant gram-negative microorganisms.
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131
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Goltermann L, Yavari N, Zhang M, Ghosal A, Nielsen PE. PNA Length Restriction of Antibacterial Activity of Peptide-PNA Conjugates in Escherichia coli Through Effects of the Inner Membrane. Front Microbiol 2019; 10:1032. [PMID: 31178830 PMCID: PMC6542938 DOI: 10.3389/fmicb.2019.01032] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/24/2019] [Indexed: 01/10/2023] Open
Abstract
Peptide Nucleic Acid (PNA)-peptide conjugates targeting essential bacterial genes are showing promise as antisense antimicrobials in drug discovery. Optimization has focused on selection of target genes and exact localization around the ribosome binding site, but surprisingly a length optimum around 10-12 nucleobases has been found. Addressing this observation, we have investigated the relationship between PNA-length, PNA-RNA duplex stability and antimicrobial activity in E. coli in more detail. For PNAs of identical length of ten nucleobases the expected reverse correlation between the thermal stability (Tm) of the PNA-RNA duplex and the MIC for single mismatched PNAs was found. Also the expected direct correlation between the length of the PNA and the PNA-RNA duplex stability was found. Nonetheless, 10-mer PNAs [in a 6-18 mer extension series of (KFF)3K- and (RXR)4 conjugates] were the most active as antisense antimicrobials in both wild type E. coli MG1655 and AS19, suggesting that the size constraint is related to the bacterial uptake of PNA-peptide conjugates. This conclusion was supported by flow cytometry data showing higher bacterial uptake of shorter PNA fluorophore labeled conjugates. Interestingly, the size-limited uptake seems independent on outer membrane integrity (AS19), and thus the results suggest that the inner membrane limits the molecular size for peptide-PNA passage.
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Affiliation(s)
- Lise Goltermann
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niloofar Yavari
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Meiqin Zhang
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anubrata Ghosal
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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132
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Pham TN, Loupias P, Dassonville-Klimpt A, Sonnet P. Drug delivery systems designed to overcome antimicrobial resistance. Med Res Rev 2019; 39:2343-2396. [PMID: 31004359 DOI: 10.1002/med.21588] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/13/2019] [Accepted: 03/31/2019] [Indexed: 02/06/2023]
Abstract
Antimicrobial resistance has emerged as a huge challenge to the effective treatment of infectious diseases. Aside from a modest number of novel anti-infective agents, very few new classes of antibiotics have been successfully developed for therapeutic use. Despite the research efforts of numerous scientists, the fight against antimicrobial (ATB) resistance has been a longstanding continued effort, as pathogens rapidly adapt and evolve through various strategies, to escape the action of ATBs. Among other mechanisms of resistance to antibiotics, the sophisticated envelopes surrounding microbes especially form a major barrier for almost all anti-infective agents. In addition, the mammalian cell membrane presents another obstacle to the ATBs that target intracellular pathogens. To negotiate these biological membranes, scientists have developed drug delivery systems to help drugs traverse the cell wall; these are called "Trojan horse" strategies. Within these delivery systems, ATB molecules can be conjugated with one of many different types of carriers. These carriers could include any of the following: siderophores, antimicrobial peptides, cell-penetrating peptides, antibodies, or even nanoparticles. In recent years, the Trojan horse-inspired delivery systems have been increasingly reported as efficient strategies to expand the arsenal of therapeutic solutions and/or reinforce the effectiveness of conventional ATBs against drug-resistant microbes, while also minimizing the side effects of these drugs. In this paper, we aim to review and report on the recent progress made in these newly prevalent ATB delivery strategies, within the current context of increasing ATB resistance.
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Affiliation(s)
- Thanh-Nhat Pham
- Université de Picardie Jules Verne, AGIR: Agents Infectieux, Résistance et Chimiothérapie, Amiens, France
| | - Pauline Loupias
- Université de Picardie Jules Verne, AGIR: Agents Infectieux, Résistance et Chimiothérapie, Amiens, France
| | | | - Pascal Sonnet
- Université de Picardie Jules Verne, AGIR: Agents Infectieux, Résistance et Chimiothérapie, Amiens, France
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133
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Abouelhassan Y, Garrison AT, Yang H, Chávez-Riveros A, Burch GM, Huigens RW. Recent Progress in Natural-Product-Inspired Programs Aimed To Address Antibiotic Resistance and Tolerance. J Med Chem 2019; 62:7618-7642. [PMID: 30951303 DOI: 10.1021/acs.jmedchem.9b00370] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacteria utilize multiple mechanisms that enable them to gain or acquire resistance to antibiotic therapies during the treatment of infections. In addition, bacteria form biofilms which are surface-attached communities of enriched populations containing persister cells encased within a protective extracellular matrix of biomolecules, leading to chronic and recurring antibiotic-tolerant infections. Antibiotic resistance and tolerance are major global problems that require innovative therapeutic strategies to address the challenges associated with pathogenic bacteria. Historically, natural products have played a critical role in bringing new therapies to the clinic to treat life-threatening bacterial infections. This Perspective provides an overview of antibiotic resistance and tolerance and highlights recent advances (chemistry, biology, drug discovery, and development) from various research programs involved in the discovery of new antibacterial agents inspired by a diverse series of natural product antibiotics.
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Affiliation(s)
- Yasmeen Abouelhassan
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy , University of Florida , Gainesville , Florida 32610 , United States
| | - Aaron T Garrison
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy , University of Florida , Gainesville , Florida 32610 , United States
| | - Hongfen Yang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy , University of Florida , Gainesville , Florida 32610 , United States
| | - Alejandra Chávez-Riveros
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy , University of Florida , Gainesville , Florida 32610 , United States
| | - Gena M Burch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy , University of Florida , Gainesville , Florida 32610 , United States
| | - Robert W Huigens
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy , University of Florida , Gainesville , Florida 32610 , United States
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134
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Knysh OV, Isayenko OY, Voyda YV, Kizimenko OO, Babych YM. Influence of cell-free extracts of Bifidobacterium bifidum and Lactobacillus reuteri on proliferation and biofilm formation by Escherichia coli and Pseudomonas aeruginosa. REGULATORY MECHANISMS IN BIOSYSTEMS 2019. [DOI: 10.15421/021938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The development of new effective preparations for the correction of microecological disorders based on probiotic derivatives requires a comprehensive study of the biological activity of the latter. We studied the proliferative activity and biofilm formation by clinical isolates: Escherichia coli and Pseudomonas aeruginosa under the influence of cell-free extracts containing structural components and metabolites of the Bifidobacterium bifidum and Lactobacillus reuteri probiotic strains. Cell-free extracts were obtained from disintegrates and cultures of probiotics. Disintegrates were prepared by cyclic freezing-thawing of probiotic cell suspensions. The cultures were obtained by cultivating probiotic microorganisms in their own disintegrates. The obtained disintegrates and cultures were filtered. The proliferative activity of the test cultures was studied using the spectrophotometric microtiter plate method after an hour-long exposure in undiluted cell-free extracts and subsequent cultivation in a nutrient medium containing 30%vol of the studied extracts at 37 °C for 24 hours. The biofilm formation of the test cultures was studied with 30% vol content of cell-free extracts in the cultivation medium using the spectrophotometric microtiter plate method. All the studied extracts exerted a similar effect on the proliferative activity and biofilm formation by E. coli and P. aeruginosa. Exposure of the test cultures in all undiluted extracts during an hour led to a significant decrease in the optical density of the test samples: optical density of the test wells ranged from 36.5% to 49.8% of the control wells. The test cultures that were exposed to the extracts: filtrate of L. reuteri disintegrate (L), filtrate of В. bifidum disintegrate (B) and filtrate of В. bifidum culture, grown in В. bifidum disintegrate (MB) after dilution and subsequent cultivation over the next 24 hours completely restored the ability to proliferate. The proliferative activity of the test cultures that were exposed to the extracts: filtrate of L. reuteri culture, grown in L. reuteri disintegrate (ML) and filtrate of L. reuteri culture, grown in L. reuteri disintegrate supplemented with 0.8 M glycerol and 0.4 M glucose (MLG), was significantly inhibited after dilution and subsequent cultivation. The inhibition indices calculated for the ML extract were: 25.9% (E. coli) and 53.0% (P. aeruginosa). Inhibition indices calculated for the MLG extract were: 62.0% (E. coli) and 96.9% (P. aeruginosa). MLG extract had more pronounced inhibitory effect on the proliferation of the test cultures than ML extract. All the studied extracts exerted significant inhibitory effect on the biofilm formation of the test cultures. Analysis of the results of the study shows that cell-free extracts of L. reuteri culture grown in its disintegrate without supplementation or supplemented with glycerol and glucose have the highest antimicrobial activity and can be used as metabiotics to prevent overgrowth of potentially pathogenic bacteria, as well as inoculation and proliferation of pathogenic gram-negative bacteria in the gastrointestinal tract. They can be used alone or in combination with cellular probiotics to enhance their probiotic action. This study encourages further careful investigation of the biochemical composition of cell-free extracts and clarifying the mechanism of their action.
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Khan F, Manivasagan P, Lee JW, Pham DTN, Oh J, Kim YM. Fucoidan-Stabilized Gold Nanoparticle-Mediated Biofilm Inhibition, Attenuation of Virulence and Motility Properties in Pseudomonas aeruginosa PAO1. Mar Drugs 2019; 17:E208. [PMID: 30987163 PMCID: PMC6520775 DOI: 10.3390/md17040208] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 12/13/2022] Open
Abstract
The emergence of antibiotic resistance in Pseudomonas aeruginosa due to biofilm formation has transformed this opportunistic pathogen into a life-threatening one. Biosynthesized nanoparticles are increasingly being recognized as an effective anti-biofilm strategy to counter P. aeruginosa biofilms. In the present study, gold nanoparticles (AuNPs) were biologically synthesized and stabilized using fucoidan, which is an active compound sourced from brown seaweed. Biosynthesized fucoidan-stabilized AuNPs (F-AuNPs) were subjected to characterization using UV-visible spectroscopy, Fourier transform infrared spectroscopy (FTIR), field emission transmission electron microscopy (FE-TEM), dynamic light scattering (DLS), and energy dispersive X-ray diffraction (EDX). The biosynthesized F-AuNPs were then evaluated for their inhibitory effects on P. aeruginosa bacterial growth, biofilm formation, virulence factor production, and bacterial motility. Overall, the activities of F-AuNPs towards P. aeruginosa were varied depending on their concentration. At minimum inhibitory concentration (MIC) (512 µg/mL) and at concentrations above MIC, F-AuNPs exerted antibacterial activity. In contrast, the sub-inhibitory concentration (sub-MIC) levels of F-AuNPs inhibited biofilm formation without affecting bacterial growth, and eradicated matured biofilm. The minimum biofilm inhibition concentration (MBIC) and minimum biofilm eradication concentration (MBEC) were identified as 128 µg/mL. Furthermore, sub-MICs of F-AuNPs also attenuated the production of several important virulence factors and impaired bacterial swarming, swimming, and twitching motilities. Findings from the present study provide important insights into the potential of F-AuNPs as an effective new drug for controlling P. aeruginosa-biofilm-related infections.
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Affiliation(s)
- Fazlurrahman Khan
- Marine-Integrated Bionics Research Center, Pukyong National University, Busan 48513, Korea.
| | | | - Jang-Won Lee
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Korea.
| | - Dung Thuy Nguyen Pham
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Korea.
| | - Junghwan Oh
- Marine-Integrated Bionics Research Center, Pukyong National University, Busan 48513, Korea.
- Department of Biomedical Engineering, Pukyong National University, Busan 48513, Korea.
| | - Young-Mog Kim
- Marine-Integrated Bionics Research Center, Pukyong National University, Busan 48513, Korea.
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Korea.
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Widya M, Pasutti WD, Sachdeva M, Simmons RL, Tamrakar P, Krucker T, Six DA. Development and Optimization of a Higher-Throughput Bacterial Compound Accumulation Assay. ACS Infect Dis 2019; 5:394-405. [PMID: 30624052 DOI: 10.1021/acsinfecdis.8b00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Gram-negative bacterial permeability barrier, coupled with efflux, raises formidable challenges to antibiotic drug discovery. The absence of efficient assays to determine compound penetration into the cell and impact of efflux makes the process resource-intensive, small-scale, and lacking much success. Here, we present BacPK: a label-free, solid phase extraction-mass spectrometry (SPE-MS)-based assay that measures total cellular compound accumulation in Escherichia coli. The BacPK assay is a 96-well accumulation assay that takes advantage of 9 s/sample SPE-MS throughput. This enables the analysis of each compound in a four-point dose-response in isogenic strain pairs along with a no-cell control and 16-point external standard curve, all in triplicate. To validate the assay, differences in accumulation were examined for tetracycline (Tet) and two analogs, confirming that close analogs can differ greatly in accumulation. Tet cellular accumulation was also compared for isogenic strains exhibiting Tet resistance due to the expression of an efflux pump (TetA) or ribosomal protection protein (TetM), confirming only TetA affected cellular Tet accumulation. Finally, using a diverse set of antibacterial compounds, we confirmed the assay's ability to quantify differences in accumulation for isogenic strain pairs with efflux or permeability alterations that are consistent with differences in susceptibility seen for the compounds.
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Durcik M, Tomašič T, Zidar N, Zega A, Kikelj D, Mašič LP, Ilaš J. ATP-competitive DNA gyrase and topoisomerase IV inhibitors as antibacterial agents. Expert Opin Ther Pat 2019; 29:171-180. [PMID: 30686070 DOI: 10.1080/13543776.2019.1575362] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION The bacterial topoisomerases DNA gyrase and topoisomerase IV are validated targets for development of novel antibacterial agents. Fluoroquinolones inhibit the catalytic GyrA and/or ParC(GrlA) subunit and have been commonly used, although these have toxicity liabilities that restrict their use. The ATPase GyrB and ParE(GrlB) subunits have been much less explored and after withdrawal of novobiocin, there are no further marketed inhibitors . ATP-competitive inhibitors of GyrB and/or ParE(GrlB) are of special interest, as this target has been validated, and it is expected that many of the problems associated with fluoroquinolones can be avoided. AREAS COVERED This review summarises the development of ATP-competitive inhibitors of GyrB and/or ParE(GrlB) as novel antibacterial agents over the last 10 years. Structural features of the new inhibitors and their optimisation strategies are highlighted. EXPERT OPINION The development of novel ATP-competitive inhibitors of GyrB and/or ParE(GrlB) is ongoing in industrial and academical research. Development of resistance is one of the most problematic issues, but GyrB/ParE(GrlB) inhibitors do not show cross-resistance with fluoroquinolones. Other common issues, such as low solubility, high protein binding, development of off-target resistance, are related to the structures of the inhibitors themselves, which is thus a main focus of design strategies. With some now in early clinical development, there is reasonable expectation that novel ATP-competitive inhibitors of GyrB/ParE(GrlB) will reach the market in the near future.
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Affiliation(s)
- Martina Durcik
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Tihomir Tomašič
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Nace Zidar
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Anamarija Zega
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Danijel Kikelj
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | | | - Janez Ilaš
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
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Bertani BR, Taylor RJ, Nagy E, Kahne D, Ruiz N. A cluster of residues in the lipopolysaccharide exporter that selects substrate variants for transport to the outer membrane. Mol Microbiol 2018; 109:541-554. [PMID: 29995974 DOI: 10.1111/mmi.14059] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2018] [Indexed: 01/03/2023]
Abstract
Most Gram-negative bacteria assemble lipopolysaccharides (LPS) on their surface to form a permeability barrier against many antimicrobials. LPS is synthesized at the inner membrane and then transported to the outer leaflet of the outer membrane. Although the overall LPS structure is conserved, LPS molecules can differ in composition at the species and strain level. Some bacteria also regulate when to modify phosphates on LPS at the inner membrane in order to become resistant to cationic antimicrobial peptides. The multi-protein Lpt trans-envelope machine, which transports LPS from the inner to the outer membrane, must therefore handle a variety of substrates. The most poorly understood step in LPS transport is how the ATP-binding cassette LptB2 FG transporter extracts LPS from the inner membrane. Here, we define residue K34 in LptG as a site within the structural cavity of the Escherichia coli LptB2 FG transporter that interacts electrostatically with phosphates on unmodified LPS. Alterations to this residue cause transport defects that are suppressed by the activation of the BasSR two-component signaling system, which results in modifications to the LPS phosphates. We also show this residue is part of a larger site in LptG that differentially contributes to the transport of unmodified and modified LPS.
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Affiliation(s)
- Blake R Bertani
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Rebecca J Taylor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Emma Nagy
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
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